diff --git a/scripts/createPanelOfNormals.R b/inst/bin/createPanelOfNormals.R
old mode 100644
new mode 100755
similarity index 99%
rename from scripts/createPanelOfNormals.R
rename to inst/bin/createPanelOfNormals.R
index ccea1f5..68366cb
--- a/scripts/createPanelOfNormals.R
+++ b/inst/bin/createPanelOfNormals.R
@@ -1,3 +1,4 @@
+#!/usr/bin/env Rscript
 library(HMMcopy)
 library(optparse)
 library(ichorCNA)
diff --git a/scripts/runIchorCNA.R b/inst/bin/runIchorCNA.R
old mode 100644
new mode 100755
similarity index 99%
rename from scripts/runIchorCNA.R
rename to inst/bin/runIchorCNA.R
index f9a99db..d61edc5
--- a/scripts/runIchorCNA.R
+++ b/inst/bin/runIchorCNA.R
@@ -1,3 +1,4 @@
+#!/usr/bin/env Rscript
 # file:   ichorCNA.R
 # author: Gavin Ha, Ph.D.
 #               Dana-Farber Cancer Institute
diff --git a/scripts/README.md b/inst/scripts/README.md
similarity index 100%
rename from scripts/README.md
rename to inst/scripts/README.md
diff --git a/scripts/example_gw_plot.png b/inst/scripts/example_gw_plot.png
similarity index 100%
rename from scripts/example_gw_plot.png
rename to inst/scripts/example_gw_plot.png
diff --git a/scripts/snakemake/README.md b/inst/scripts/snakemake/README.md
similarity index 100%
rename from scripts/snakemake/README.md
rename to inst/scripts/snakemake/README.md
diff --git a/scripts/snakemake/config/cluster.sh b/inst/scripts/snakemake/config/cluster.sh
similarity index 100%
rename from scripts/snakemake/config/cluster.sh
rename to inst/scripts/snakemake/config/cluster.sh
diff --git a/scripts/snakemake/config/config.yaml b/inst/scripts/snakemake/config/config.yaml
similarity index 100%
rename from scripts/snakemake/config/config.yaml
rename to inst/scripts/snakemake/config/config.yaml
diff --git a/scripts/snakemake/config/config_hg38.yaml b/inst/scripts/snakemake/config/config_hg38.yaml
similarity index 100%
rename from scripts/snakemake/config/config_hg38.yaml
rename to inst/scripts/snakemake/config/config_hg38.yaml
diff --git a/scripts/snakemake/config/samples.yaml b/inst/scripts/snakemake/config/samples.yaml
similarity index 100%
rename from scripts/snakemake/config/samples.yaml
rename to inst/scripts/snakemake/config/samples.yaml
diff --git a/scripts/snakemake/ichorCNA.snakefile b/inst/scripts/snakemake/ichorCNA.snakefile
similarity index 100%
rename from scripts/snakemake/ichorCNA.snakefile
rename to inst/scripts/snakemake/ichorCNA.snakefile